Influence of irrigation on the distribution and control of the nematode Meloidogyne javanica by the biocontrol bacterium Pasteuria penetrans in the field

Pasteuria penetrans, a bacterial parasite of plant-parasitic nematodes, is used to control root-knot nematode Meloidogyne spp. populations in vegetable crops. But its efficiency is variable, mostly because of the patchy distribution of the bacteria in arable fields. As the infective P. penetrans are non-motile bacteria in soil, abiotic soil factors can affect the bacteria–nematode relationships. An epidemiological study, conducted in a vegetable field, showed that abiotic factors such as irrigation, soil water holding capacity and texture, affected the efficiency of P. penetrans. A correspondence analysis between these abiotic factors and the density of P. penetrans spores in the soil, and the proportion of Meloidogyne javanica juveniles infected by the bacteria, revealed that irrigation affected directly the distribution of the spores in soil pores related to their passive transport by water flow. Laboratory experiments conducted on the passive transport of spores confirmed that intensive irrigation leached the spores down the soil profile and decreased the percentage of infected Meloidogyne juveniles.     

Improved sample preparation to determine acrylamide in difficult matrixes such as chocolate powder, cocoa, and coffee by liquid chromatography tandem mass spectroscopy

An improved sample preparation (extraction and cleanup) is presented that enables the quantification of low levels of acrylamide in difficult matrixes, including soluble chocolate powder, cocoa, coffee, and coffee surrogate. Final analysis is done by isotope-dilution liquid chromatography-electrospray ionization tandem mass spectrometry (LC-MS/MS) using d3-acrylamide as internal standard. Sample pretreatment essentially encompasses (a) protein precipitation with Carrez I and II solutions, (b) extraction of the analyte into ethyl acetate, and (c) solid-phase extraction on a Multimode cartridge. The stability of acrylamide in final extracts and in certain commercial foods and beverages is also reported. This approach provided good performance in terms of linearity, accuracy and precision. Full validation was conducted in soluble chocolate powder, achieving a decision limit (CCalpha) and detection capability (CCbeta) of 9.2 and 12.5 microg/kg, respectively. The method was extended to the analysis of acrylamide in various foodstuffs such as mashed potatoes, crisp bread, and butter biscuit and cookies. Furthermore, the accuracy of the method is demonstrated by the results obtained in three inter-laboratory proficiency tests.     

Traces of human migrations in Helicobacter pylori populations

Helicobacter pylori, a chronic gastric pathogen of human beings, can be divided into seven populations and subpopulations with distinct geographical distributions. These modern populations derive their gene pools from ancestral populations that arose in Africa, Central Asia, and East Asia. Subsequent spread can be attributed to human migratory fluxes such as the prehistoric colonization of Polynesia and the Americas, the neolithic introduction of farming to Europe, the Bantu expansion within Africa, and the slave trade.     

Class II aminoacyl transfer RNA synthetases: crystal structure of yeast aspartyl-tRNA synthetase complexed with tRNA(Asp)

The crystal structure of the binary complex tRNA(Asp)-aspartyl tRNA synthetase from yeast was solved with the use of multiple isomorphous replacement to 3 angstrom resolution. The dimeric synthetase, a member of class II aminoacyl tRNA synthetases (aaRS's) exhibits the characteristic signature motifs conserved in eight aaRS's. These three sequence motifs are contained in the catalytic site domain, built around an antiparallel beta sheet, and flanked by three alpha helices that form the pocket in which adenosine triphosphate (ATP) and the CCA end of tRNA bind. The tRNA(Asp) molecule approaches the synthetase from the variable loop side. The two major contact areas are with the acceptor end and the anticodon stem and loop. In both sites the protein interacts with the tRNA from the major groove side. The correlation between aaRS class II and the initial site of aminoacylation at 3'-OH can be explained by the structure. The molecular association leads to the following features: (i) the backbone of the GCCA single-stranded portion of the acceptor end exhibits a regular helical conformation; (ii) the loop between residues 320 and 342 in motif 2 interacts with the acceptor stem in the major groove and is in contact with the discriminator base G and the first base pair UA; and (iii) the anticodon loop undergoes a large conformational change in order to bind the protein. The conformation of the tRNA molecule in the complex is dictated more by the interaction with the protein than by its own sequence.     

CoRoT measures solar-like oscillations and granulation in stars hotter than the Sun

Oscillations of the Sun have been used to understand its interior structure. The extension of similar studies to more distant stars has raised many difficulties despite the strong efforts of the international community over the past decades. The CoRoT (Convection Rotation and Planetary Transits) satellite, launched in December 2006, has now measured oscillations and the stellar granulation signature in three main sequence stars that are noticeably hotter than the sun. The oscillation amplitudes are about 1.5 times as large as those in the Sun; the stellar granulation is up to three times as high. The stellar amplitudes are about 25% below the theoretic values, providing a measurement of the nonadiabaticity of the process ruling the oscillations in the outer layers of the stars.     

Determinants of bird community composition on patches in the suburbs of Paris, France

The ecological processes responsible for the spatial assemblages of breeding bird communities in urban landscapes are more and more investigated. Indeed, understanding these processes is imperative to plan relevant management policies. We investigated breeding bird communities on 67 patches in the suburbs of Paris, France. We examined the role of patch characteristics and geographic distance between patches in determining similarity between bird assemblages. To do this, we proposed a new SØrensen similarity index based on estimators of change in community composition taking into account the detection probability of species. The patch occupancy by sedentary and migratory species was also estimated to compare their sensitivity to urbanization. Patches close to each other supported more similar bird assemblages, suggesting an effect of the spatial distribution of patches on bird dispersal and a posteriori on local community composition. Accounting for spatial location of patches, bird assemblage similarity was related to the similarity of the surrounding level of urbanization but not to the similarity of patch size or to the similarity of patch vegetation. The mean estimated occupancy rate of sedentary species was higher than that of migratory species in the whole study area. While sedentary species occupied patches surrounded by both moderate and high levels of urbanization, migratory ones primarily occupied patches surrounded by moderate levels of urbanization. Human choices in degrees, styles, and extent of urbanization, including designation and design of patches within an urban matrix, affect the composition of local bird communities.     

Effect of aging on lees and of three different dry yeast derivative products on Verdejo white wine composition and sensorial characteristics

A study was made of the effect of aging on lees and of three different commercial yeast derivative products of different composition and degree of purification on the phenolic compounds, color, proteins, polysaccharides, and sensorial characteristics of white wines. The results obtained showed that the lees and yeast derivative products can interact or adsorb some of the phenolic compounds present in wines, reducing their concentration. This reduction depends on the treatment applied, the phenolic compound analyzed, and the stage of vinification or aging process. The use of lees and yeast derivative products can reduce the color intensity and the browning of the wines immediately following treatment. The monosaccharide and polysaccharide content of yeast derivative products depends on the manufacturing process and degree of purification of the product, both of which have an influence on wine treatments. After 6 months in the bottle, both the aging on lees and the treatment with commercial yeast derivative products gave rise to wines with better sensorial characteristics than in the case of the control wines.     

Compared effects of long-term pig slurry applications and mineral fertilization on soil denitrification and its end products (N2O, N2)

The long-term (9 years) effect of pig slurry applications vs mineral fertilization on denitrifying activity, N₂O production and soil organic carbon (C) (extractable C, microbial biomass C and total organic C) was compared at three soil depths of adjacent plots. The denitrifying activities were measured on undisturbed soil cores and on sieved soil samples with acetylene method to estimate denitrification rates under field or potential conditions. Pig slurry applications had a moderate impact on the C pools. Total organic C was increased by +6.5% and microbial biomass C by ≥25%. The potential denitrifying activity on soil suspension was stimulated (×1.8, P<0.05) 12 days after the last slurry application. This stimulation was still apparent, but not significant, 10 months later and, according to both methods of denitrifying activity measurement (r ²=0.916, P<0.01 on sieved soil; r ²=0.845, P<0.001 on soil cores), was associated with an increase in microbial biomass C above a threshold of about 105 mg kg⁻¹. The effect of pig slurry on denitrification and N₂O reduction rates was detected on the surface layer (0–20 cm) only. However, no pig slurry effect could be detected on soil cores at field conditions or after NO₃ ⁻ enrichments at 20°C. Although the potential denitrifying activity in sieved soil samples was stimulated, the N₂O production was lower (P<0.03) in the plot fertilized with pig slurry, indicating a lower N₂O/(N₂O + N₂) ratio of the released gases. The pig-slurry-fertilized plot also showed a higher N₂O reduction activity, which is coherent with the lower N₂O production in anaerobiosis.